def test_to_xyz(self):
fragment = Fragment(-2, 2)
# to_xyz() should return empty string when no atoms are added to fragment
self.assertEqual(fragment.to_xyz(), "")
atom0 = Atom("H", 0, 0, 0)
fragment.add_atom(atom0)
# to_xyz() should return string of first atom after only 1 atom added
self.assertEqual(fragment.to_xyz(), atom0.to_xyz() + "\n")
atom1 = Atom("Cl", 5, 7, -3)
fragment.add_atom(atom1)
# to_xyz() should return string of 2 atoms after 2nd atom added
self.assertEqual(fragment.to_xyz(),
atom1.to_xyz() + "\n" + atom0.to_xyz() + "\n")
atom2 = Atom("Xe", 10.234235, -0.00000234, 2.353523)
fragment.add_atom(atom2)
# to_xyz() should return string of 3 atoms after only 3rd atom added
self.assertEqual(
fragment.to_xyz(),
atom1.to_xyz() + "\n" + atom0.to_xyz() + "\n" + atom2.to_xyz() +
"\n")
def test_to_standard_xyz(self):
molecule = Molecule()
fragment0 = Fragment(-1, 1)
fragment0.add_atom(Atom("H", 5, 3, 0.00343))
fragment0.add_atom(Atom("Cl", 2, 0, -13))
fragment0.add_atom(Atom("He", 6, 2, 0.343))
molecule.add_fragment(fragment0)
self.assertEqual(molecule.to_xyz(), fragment0.to_xyz()[:-1])
fragment1 = Fragment(-2, 1)
fragment1.add_atom(Atom("Ar", 0.23430523424, -34, -234.5235))
molecule.add_fragment(fragment1)
self.assertEqual(molecule.to_xyz(),
fragment1.to_xyz() + fragment0.to_xyz()[:-1])
fragment2 = Fragment(0, 2)
fragment2.add_atom(Atom("Xe", 0, 0, 0))
fragment2.add_atom(Atom("Br", 62, 5, 0.001))
molecule.add_fragment(fragment2)
self.assertEqual(
molecule.to_xyz(),
fragment1.to_xyz() + fragment2.to_xyz() + fragment0.to_xyz()[:-1])